Likelihood of drowning en route to Europe spirals to one in 88, says UN, with most deaths reported off Libyan shore.

About half of the 327,800 refugees who crossed the Mediterranean this year did so using the Libya-Italy route [EPA]

At least 3,800 refugees have died in the Mediterranean Sea while trying to reach Europe so far this year, making 2016 the deadliest year on record, according to the UN refugee agency.

William Spindler, the spokesman for the Geneva-based agency, announced the grim milestone on Twitter on Wednesday.

"We're receiving more reports of deaths in the Med," Spindler tweeted on Wednesday.

"We can now confirm that at least 3,800 people have died, making 2016 the deadliest ever."

"From one death for every 269 arrivals last year, in 2016 the likelihood of dying has spiralled to one in 88," he added in a statement published on the agency's website.

More refugee deaths were reported off the Libyan shore on Wednesday, as the EU’s border and coastguard agency Frontex warned that rescue missions near the troubled North African nation were getting ever more dangerous.

The Doctors Without Borders (MSF) charity said one of its latest rescue vessels picked up 25 bodies and 107 survivors from an overcrowded rubber boat some 48 kilometres off the coast of Libya.

"Sea rescue operations are becoming a race through a maritime graveyard," the head of MSF migration operations, Stefano Argenziano, said in an online statement.

Refugee deaths have been piling as the fragile and often overcrowded boats carrying refugees in the Mediterranean capsize or sink.

For the rise in the number of deaths, the UN refugee agency blames bad weather, flimsy boats and the fact that refugees are increasingly taking the hazardous central Mediterranean route from Libya to Italy.

A deal between the EU and Turkey largely closed off the eastern route from Middle East to Europe through Turkey earlier this year.